Starting phenix.real_space_refine on Sat Jul 4 12:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxm_23571/07_2026/7lxm_23571.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12987 2.51 5 N 3351 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "E" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "P" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "O" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.21 Number of scatterers: 20820 At special positions: 0 Unit cell: (149.796, 154.926, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4368 8.00 N 3351 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.15 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.18 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.15 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.16 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 7 " - " MAN G 8 " " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN a 7 " - " MAN a 8 " " MAN g 4 " - " MAN g 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN o 7 " - " MAN o 8 " " MAN u 4 " - " MAN u 5 " " MAN x 4 " - " MAN x 5 " " MAN x 5 " - " MAN x 6 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA a 3 " - " MAN a 7 " " MAN a 4 " - " MAN a 5 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 7 " " MAN o 4 " - " MAN o 5 " " BMA u 3 " - " MAN u 4 " " BMA x 3 " - " MAN x 4 " " MAN x 7 " - " MAN x 8 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " MAN G 5 " - " MAN G 6 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA a 3 " - " MAN a 4 " " MAN a 5 " - " MAN a 6 " " BMA g 3 " - " MAN g 6 " " MAN g 6 " - " MAN g 7 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA o 3 " - " MAN o 4 " " MAN o 5 " - " MAN o 6 " " BMA u 3 " - " MAN u 6 " " MAN u 6 " - " MAN u 7 " " BMA w 3 " - " MAN w 4 " " BMA x 3 " - " MAN x 7 " " MAN x 7 " - " MAN x 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN E 197 " " NAG 1 1 " - " ASN E 276 " " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 289 " " NAG C 602 " - " ASN C 392 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 392 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 138 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN A 197 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN C 138 " " NAG b 1 " - " ASN C 88 " " NAG c 1 " - " ASN C 130 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 386 " " NAG l 1 " - " ASN C 448 " " NAG m 1 " - " ASN C 197 " " NAG n 1 " - " ASN C 276 " " NAG o 1 " - " ASN E 138 " " NAG p 1 " - " ASN E 88 " " NAG q 1 " - " ASN E 130 " " NAG r 1 " - " ASN E 160 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 295 " " NAG w 1 " - " ASN E 301 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 448 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 810.3 milliseconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 45 sheets defined 21.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.184A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.725A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.937A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.834A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.140A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.242A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.887A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.958A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.214A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.645A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.899A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.841A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.133A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.354A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.505A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 651 through 660 removed outlier: 3.605A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.143A pdb=" N ASN N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 65 No H-bonds generated for 'chain 'N' and resid 63 through 65' Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 351 removed outlier: 3.636A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.903A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.770A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.144A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.502A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.508A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 Processing helix chain 'F' and resid 651 through 660 removed outlier: 3.607A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.173A pdb=" N ASN P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 4.082A pdb=" N GLY P 55 " --> pdb=" O HIS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.792A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.641A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.658A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.631A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.588A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 302 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.588A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 441 through 456 current: chain 'A' and resid 413 through 420 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.198A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.568A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.127A pdb=" N CYS H 92 " --> pdb=" O TRP H 101 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP H 101 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR H 94 " --> pdb=" O ASP H 100Q" (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.446A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.750A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.668A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.735A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.634A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 302 current: chain 'C' and resid 357 through 361 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.714A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 441 through 456 current: chain 'C' and resid 413 through 420 Processing sheet with id=AC7, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.499A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.127A pdb=" N CYS N 92 " --> pdb=" O TRP N 101 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP N 101 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR N 94 " --> pdb=" O ASP N 100Q" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.397A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.744A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.626A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.713A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.628A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE3, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.709A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 441 through 456 current: chain 'E' and resid 413 through 420 Processing sheet with id=AE4, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.517A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 11 through 12 removed outlier: 7.109A pdb=" N CYS P 92 " --> pdb=" O TRP P 101 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP P 101 " --> pdb=" O CYS P 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR P 94 " --> pdb=" O ASP P 100Q" (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.391A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 19 through 23 728 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5038 1.32 - 1.47: 7214 1.47 - 1.61: 8835 1.61 - 1.75: 9 1.75 - 1.89: 138 Bond restraints: 21234 Sorted by residual: bond pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 1.808 1.613 0.195 3.30e-02 9.18e+02 3.49e+01 bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.615 0.193 3.30e-02 9.18e+02 3.43e+01 bond pdb=" CA THR E 137 " pdb=" C THR E 137 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.33e-02 5.65e+03 2.76e+01 bond pdb=" CB PHE C 159 " pdb=" CG PHE C 159 " ideal model delta sigma weight residual 1.502 1.384 0.118 2.30e-02 1.89e+03 2.62e+01 bond pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.61e+01 ... (remaining 21229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 24984 2.55 - 5.09: 3426 5.09 - 7.64: 379 7.64 - 10.19: 65 10.19 - 12.73: 12 Bond angle restraints: 28866 Sorted by residual: angle pdb=" CA PHE A 159 " pdb=" CB PHE A 159 " pdb=" CG PHE A 159 " ideal model delta sigma weight residual 113.80 122.57 -8.77 1.00e+00 1.00e+00 7.69e+01 angle pdb=" CA PHE C 159 " pdb=" CB PHE C 159 " pdb=" CG PHE C 159 " ideal model delta sigma weight residual 113.80 122.51 -8.71 1.00e+00 1.00e+00 7.60e+01 angle pdb=" CA PHE E 159 " pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 113.80 122.49 -8.69 1.00e+00 1.00e+00 7.55e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.09 -8.22 1.04e+00 9.25e-01 6.25e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.08 -8.21 1.04e+00 9.25e-01 6.23e+01 ... (remaining 28861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 11142 17.57 - 35.14: 294 35.14 - 52.70: 81 52.70 - 70.27: 29 70.27 - 87.84: 13 Dihedral angle restraints: 11559 sinusoidal: 4683 harmonic: 6876 Sorted by residual: dihedral pdb=" C PHE C 159 " pdb=" N PHE C 159 " pdb=" CA PHE C 159 " pdb=" CB PHE C 159 " ideal model delta harmonic sigma weight residual -122.60 -107.87 -14.73 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" C PHE A 159 " pdb=" N PHE A 159 " pdb=" CA PHE A 159 " pdb=" CB PHE A 159 " ideal model delta harmonic sigma weight residual -122.60 -107.96 -14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C PHE E 159 " pdb=" N PHE E 159 " pdb=" CA PHE E 159 " pdb=" CB PHE E 159 " ideal model delta harmonic sigma weight residual -122.60 -108.02 -14.58 0 2.50e+00 1.60e-01 3.40e+01 ... (remaining 11556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2533 0.108 - 0.216: 1010 0.216 - 0.324: 142 0.324 - 0.432: 32 0.432 - 0.540: 6 Chirality restraints: 3723 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.54e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.43e+02 ... (remaining 3720 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.094 2.00e-02 2.50e+03 9.89e-02 1.22e+02 pdb=" CG ASN D 611 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.159 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.094 2.00e-02 2.50e+03 9.87e-02 1.22e+02 pdb=" CG ASN F 611 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.094 2.00e-02 2.50e+03 9.85e-02 1.21e+02 pdb=" CG ASN B 611 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.116 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2997 2.73 - 3.28: 18807 3.28 - 3.82: 34213 3.82 - 4.36: 41635 4.36 - 4.90: 67793 Nonbonded interactions: 165445 Sorted by model distance: nonbonded pdb=" O4 MAN G 5 " pdb=" O6 MAN G 5 " model vdw 2.194 3.040 nonbonded pdb=" O4 MAN o 8 " pdb=" O6 MAN o 8 " model vdw 2.232 3.040 nonbonded pdb=" O5 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.255 2.432 nonbonded pdb=" O4 MAN o 5 " pdb=" O6 MAN o 5 " model vdw 2.257 3.040 nonbonded pdb=" O4 MAN a 5 " pdb=" O6 MAN a 5 " model vdw 2.270 3.040 ... (remaining 165440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'S' and resid 4 through 7) selection = (chain 'V' and resid 6 through 9) selection = (chain 'a' and resid 5 through 8) selection = (chain 'g' and resid 4 through 7) selection = (chain 'j' and resid 6 through 9) selection = (chain 'o' and resid 5 through 8) selection = (chain 'u' and resid 4 through 7) selection = (chain 'x' and resid 6 through 9) } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'k' selection = chain 'l' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.195 21432 Z= 1.090 Angle : 1.856 13.558 29421 Z= 1.125 Chirality : 0.111 0.540 3723 Planarity : 0.009 0.051 3429 Dihedral : 9.904 87.840 6996 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.20 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 0.19 % Favored : 99.57 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2325 helix: -0.63 (0.25), residues: 396 sheet: 0.83 (0.19), residues: 708 loop : 0.97 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 66 TYR 0.045 0.007 TYR N 100O PHE 0.057 0.009 PHE A 159 TRP 0.047 0.009 TRP A 96 HIS 0.008 0.002 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.01995 / 1.05 (21234) covalent geometry : angle 1.79975 / 1.12 (28866) SS BOND : bond 0.04797 / 3.53 ( 39) SS BOND : angle 3.37946 / 2.11 ( 78) hydrogen bonds : bond 0.16285 / 10.60 ( 689) hydrogen bonds : angle 7.62873 / 5.20 ( 1842) link_ALPHA1-2 : bond 0.06652 / 3.97 ( 12) link_ALPHA1-2 : angle 4.75431 / 3.20 ( 36) link_ALPHA1-3 : bond 0.06026 / 3.69 ( 15) link_ALPHA1-3 : angle 5.61496 / 3.71 ( 45) link_ALPHA1-6 : bond 0.05868 / 3.69 ( 21) link_ALPHA1-6 : angle 3.33774 / 2.29 ( 63) link_BETA1-4 : bond 0.06091 / 4.01 ( 60) link_BETA1-4 : angle 4.02336 / 2.98 ( 180) link_NAG-ASN : bond 0.07544 / 4.76 ( 51) link_NAG-ASN : angle 2.68420 / 1.82 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 518 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7848 (mmm160) REVERT: A 99 ASN cc_start: 0.8375 (t0) cc_final: 0.8026 (t0) REVERT: A 325 ASP cc_start: 0.8135 (m-30) cc_final: 0.7866 (m-30) REVERT: H 13 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7800 (mmmt) REVERT: H 100 LYS cc_start: 0.7839 (mttt) cc_final: 0.7500 (mtpp) REVERT: L 58 ILE cc_start: 0.8515 (mm) cc_final: 0.8258 (mm) REVERT: C 46 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7412 (mtmm) REVERT: C 66 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7766 (tpt170) REVERT: C 103 GLN cc_start: 0.8005 (tt0) cc_final: 0.7795 (tt0) REVERT: D 608 VAL cc_start: 0.7631 (t) cc_final: 0.7409 (m) REVERT: D 625 ASN cc_start: 0.7414 (m-40) cc_final: 0.7048 (t0) REVERT: N 13 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7882 (mmmt) REVERT: N 100 LYS cc_start: 0.7946 (mttt) cc_final: 0.7630 (mtpp) REVERT: E 46 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7273 (mtmm) REVERT: E 66 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7919 (mmm160) REVERT: E 99 ASN cc_start: 0.8205 (t0) cc_final: 0.7875 (t0) REVERT: E 348 LYS cc_start: 0.7335 (tptt) cc_final: 0.6509 (mptt) REVERT: E 498 PRO cc_start: 0.6550 (Cg_endo) cc_final: 0.6243 (Cg_exo) REVERT: P 13 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7929 (mmmt) REVERT: P 100 LYS cc_start: 0.7886 (mttt) cc_final: 0.7528 (mtpp) outliers start: 5 outliers final: 5 residues processed: 523 average time/residue: 0.1597 time to fit residues: 122.5281 Evaluate side-chains 284 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 279 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain E residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 650 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN F 650 GLN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140078 restraints weight = 29849.640| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.65 r_work: 0.3389 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 21432 Z= 0.188 Angle : 0.846 10.907 29421 Z= 0.403 Chirality : 0.050 0.325 3723 Planarity : 0.005 0.058 3429 Dihedral : 5.486 31.723 2548 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.51 % Favored : 98.37 % Rotamer: Outliers : 2.42 % Allowed : 7.69 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2325 helix: 0.66 (0.28), residues: 351 sheet: 0.55 (0.19), residues: 669 loop : 0.36 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 350 TYR 0.017 0.002 TYR N 91 PHE 0.019 0.003 PHE E 391 TRP 0.026 0.002 TRP A 479 HIS 0.007 0.002 HIS N 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (21234) covalent geometry : angle 0.76061 / 0.39 (28866) SS BOND : bond 0.00482 / 0.31 ( 39) SS BOND : angle 1.26973 / 0.86 ( 78) hydrogen bonds : bond 0.05160 / 3.40 ( 689) hydrogen bonds : angle 6.27650 / 4.30 ( 1842) link_ALPHA1-2 : bond 0.01609 / 1.02 ( 12) link_ALPHA1-2 : angle 3.15541 / 2.05 ( 36) link_ALPHA1-3 : bond 0.01289 / 0.81 ( 15) link_ALPHA1-3 : angle 3.52585 / 2.26 ( 45) link_ALPHA1-6 : bond 0.00693 / 0.41 ( 21) link_ALPHA1-6 : angle 1.58744 / 1.08 ( 63) link_BETA1-4 : bond 0.00678 / 0.45 ( 60) link_BETA1-4 : angle 3.08624 / 2.30 ( 180) link_NAG-ASN : bond 0.00550 / 0.36 ( 51) link_NAG-ASN : angle 3.07827 / 2.12 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 354 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 LYS cc_start: 0.7632 (tptt) cc_final: 0.6784 (mptt) REVERT: H 13 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7826 (mmmt) REVERT: H 77 LEU cc_start: 0.8022 (mm) cc_final: 0.7608 (mm) REVERT: H 100 LYS cc_start: 0.7928 (mttt) cc_final: 0.7611 (mtpp) REVERT: L 25 GLU cc_start: 0.7895 (pp20) cc_final: 0.7531 (pp20) REVERT: C 350 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5975 (ttm-80) REVERT: N 13 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7924 (mmmt) REVERT: N 77 LEU cc_start: 0.7778 (mm) cc_final: 0.7439 (mm) REVERT: N 100 LYS cc_start: 0.8034 (mttt) cc_final: 0.7759 (mtpp) REVERT: E 66 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7838 (mmm160) REVERT: E 99 ASN cc_start: 0.8222 (t0) cc_final: 0.7943 (t0) REVERT: E 195 ASN cc_start: 0.7349 (p0) cc_final: 0.7100 (p0) REVERT: F 653 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8076 (mm-40) REVERT: P 13 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7842 (mmmt) REVERT: P 29 VAL cc_start: 0.8160 (p) cc_final: 0.7837 (t) REVERT: P 66 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6945 (ptm-80) REVERT: P 77 LEU cc_start: 0.7949 (mm) cc_final: 0.7683 (mm) REVERT: P 81 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.6901 (mtt90) REVERT: P 100 LYS cc_start: 0.7956 (mttt) cc_final: 0.7609 (mtpp) REVERT: O 25 GLU cc_start: 0.7696 (pp20) cc_final: 0.7469 (pp20) REVERT: O 51 ASN cc_start: 0.7770 (m-40) cc_final: 0.7539 (m-40) outliers start: 51 outliers final: 25 residues processed: 389 average time/residue: 0.1482 time to fit residues: 86.8362 Evaluate side-chains 301 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 114 GLN ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.165922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139955 restraints weight = 29976.505| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.93 r_work: 0.3365 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21432 Z= 0.162 Angle : 0.769 9.999 29421 Z= 0.361 Chirality : 0.048 0.392 3723 Planarity : 0.004 0.067 3429 Dihedral : 5.029 23.944 2538 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.18 % Allowed : 10.16 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2325 helix: 0.78 (0.28), residues: 351 sheet: 0.41 (0.18), residues: 663 loop : 0.16 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 20 TYR 0.014 0.001 TYR P 91 PHE 0.016 0.002 PHE H 100K TRP 0.021 0.002 TRP B 631 HIS 0.005 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (21234) covalent geometry : angle 0.69048 / 0.34 (28866) SS BOND : bond 0.00470 / 0.31 ( 39) SS BOND : angle 1.06338 / 0.70 ( 78) hydrogen bonds : bond 0.04163 / 2.75 ( 689) hydrogen bonds : angle 5.90791 / 4.07 ( 1842) link_ALPHA1-2 : bond 0.01422 / 0.88 ( 12) link_ALPHA1-2 : angle 3.17872 / 2.06 ( 36) link_ALPHA1-3 : bond 0.01080 / 0.66 ( 15) link_ALPHA1-3 : angle 3.41851 / 2.22 ( 45) link_ALPHA1-6 : bond 0.00626 / 0.37 ( 21) link_ALPHA1-6 : angle 1.47302 / 0.97 ( 63) link_BETA1-4 : bond 0.00725 / 0.48 ( 60) link_BETA1-4 : angle 2.69764 / 2.04 ( 180) link_NAG-ASN : bond 0.00512 / 0.36 ( 51) link_NAG-ASN : angle 2.80342 / 1.86 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7602 (mmm160) cc_final: 0.6958 (tpm170) REVERT: A 225 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8042 (mt) REVERT: A 348 LYS cc_start: 0.7787 (tptt) cc_final: 0.6919 (mptt) REVERT: B 592 LEU cc_start: 0.8738 (tp) cc_final: 0.8421 (mp) REVERT: B 628 TRP cc_start: 0.7465 (m100) cc_final: 0.7232 (m100) REVERT: B 647 GLU cc_start: 0.5359 (tt0) cc_final: 0.5034 (tt0) REVERT: H 13 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7847 (mmmt) REVERT: H 30 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7736 (tpp80) REVERT: H 77 LEU cc_start: 0.8049 (mm) cc_final: 0.7561 (mm) REVERT: H 100 LYS cc_start: 0.7976 (mttt) cc_final: 0.7648 (mtpp) REVERT: L 25 GLU cc_start: 0.7739 (pp20) cc_final: 0.7499 (pp20) REVERT: C 66 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7694 (tpm170) REVERT: C 67 ASN cc_start: 0.7489 (t0) cc_final: 0.7137 (t0) REVERT: N 13 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7973 (mmmt) REVERT: N 77 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (mm) REVERT: N 100 LYS cc_start: 0.8046 (mttt) cc_final: 0.7757 (mtpp) REVERT: E 99 ASN cc_start: 0.8186 (t0) cc_final: 0.7953 (t0) REVERT: F 542 ARG cc_start: 0.7835 (tpt-90) cc_final: 0.7624 (ttt-90) REVERT: P 13 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7830 (mmmt) REVERT: P 66 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6963 (ptm-80) REVERT: P 81 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7010 (mtt90) REVERT: P 100 LYS cc_start: 0.8009 (mttt) cc_final: 0.7675 (mtpp) outliers start: 46 outliers final: 23 residues processed: 326 average time/residue: 0.1432 time to fit residues: 70.7492 Evaluate side-chains 284 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 50 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137617 restraints weight = 30120.917| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.97 r_work: 0.3301 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21432 Z= 0.181 Angle : 0.748 9.726 29421 Z= 0.348 Chirality : 0.049 0.338 3723 Planarity : 0.005 0.078 3429 Dihedral : 4.954 24.219 2538 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.52 % Allowed : 10.21 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2325 helix: 0.49 (0.27), residues: 369 sheet: 0.31 (0.19), residues: 642 loop : -0.07 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 30 TYR 0.014 0.002 TYR A 486 PHE 0.021 0.002 PHE H 100K TRP 0.021 0.002 TRP B 571 HIS 0.005 0.001 HIS H 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (21234) covalent geometry : angle 0.67663 / 0.33 (28866) SS BOND : bond 0.00504 / 0.33 ( 39) SS BOND : angle 1.08422 / 0.70 ( 78) hydrogen bonds : bond 0.03908 / 2.57 ( 689) hydrogen bonds : angle 5.74088 / 3.96 ( 1842) link_ALPHA1-2 : bond 0.01253 / 0.80 ( 12) link_ALPHA1-2 : angle 3.02252 / 1.96 ( 36) link_ALPHA1-3 : bond 0.00914 / 0.55 ( 15) link_ALPHA1-3 : angle 3.19502 / 2.08 ( 45) link_ALPHA1-6 : bond 0.00435 / 0.28 ( 21) link_ALPHA1-6 : angle 1.52775 / 1.02 ( 63) link_BETA1-4 : bond 0.00658 / 0.44 ( 60) link_BETA1-4 : angle 2.63518 / 1.99 ( 180) link_NAG-ASN : bond 0.00442 / 0.29 ( 51) link_NAG-ASN : angle 2.53456 / 1.72 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7584 (mmm160) cc_final: 0.6951 (tpm170) REVERT: A 225 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7955 (mt) REVERT: A 348 LYS cc_start: 0.7740 (tptt) cc_final: 0.6903 (mptt) REVERT: B 626 MET cc_start: 0.6798 (mtt) cc_final: 0.6513 (mtp) REVERT: H 13 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7952 (mmmt) REVERT: H 30 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7751 (tpp80) REVERT: H 66 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7715 (ptm160) REVERT: H 73 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7798 (ttmm) REVERT: H 77 LEU cc_start: 0.7951 (mm) cc_final: 0.7541 (mm) REVERT: H 100 LYS cc_start: 0.8099 (mttt) cc_final: 0.7746 (mtpp) REVERT: L 25 GLU cc_start: 0.7765 (pp20) cc_final: 0.7475 (pp20) REVERT: C 69 TRP cc_start: 0.8704 (m-90) cc_final: 0.8489 (m-90) REVERT: C 428 GLN cc_start: 0.8766 (mp10) cc_final: 0.7972 (mp10) REVERT: D 542 ARG cc_start: 0.8084 (tpt-90) cc_final: 0.7856 (ttt-90) REVERT: N 13 LYS cc_start: 0.8268 (mmtt) cc_final: 0.8042 (mmmt) REVERT: N 77 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7470 (mm) REVERT: N 100 LYS cc_start: 0.8196 (mttt) cc_final: 0.7909 (mtpp) REVERT: M 25 GLU cc_start: 0.7592 (pp20) cc_final: 0.7376 (pp20) REVERT: E 46 LYS cc_start: 0.7862 (mttm) cc_final: 0.7473 (mttp) REVERT: E 99 ASN cc_start: 0.8245 (t0) cc_final: 0.8032 (t0) REVERT: P 13 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7885 (mmmt) REVERT: P 66 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7125 (ptm-80) REVERT: P 81 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7040 (mtt90) REVERT: P 100 LYS cc_start: 0.8158 (mttt) cc_final: 0.7843 (mtpp) REVERT: O 25 GLU cc_start: 0.7662 (pp20) cc_final: 0.7448 (pp20) outliers start: 53 outliers final: 29 residues processed: 326 average time/residue: 0.1375 time to fit residues: 68.8461 Evaluate side-chains 296 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 184 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 591 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 300 ASN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138157 restraints weight = 29759.882| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.26 r_work: 0.3358 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21432 Z= 0.128 Angle : 0.702 9.870 29421 Z= 0.326 Chirality : 0.046 0.345 3723 Planarity : 0.004 0.081 3429 Dihedral : 4.794 23.231 2538 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.28 % Allowed : 11.25 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2325 helix: 0.73 (0.28), residues: 369 sheet: 0.40 (0.20), residues: 573 loop : -0.11 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 444 TYR 0.016 0.001 TYR A 486 PHE 0.015 0.002 PHE E 159 TRP 0.034 0.001 TRP D 610 HIS 0.004 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21234) covalent geometry : angle 0.62842 / 0.31 (28866) SS BOND : bond 0.00298 / 0.20 ( 39) SS BOND : angle 1.51473 / 1.01 ( 78) hydrogen bonds : bond 0.03453 / 2.28 ( 689) hydrogen bonds : angle 5.44217 / 3.77 ( 1842) link_ALPHA1-2 : bond 0.01202 / 0.75 ( 12) link_ALPHA1-2 : angle 2.89233 / 1.85 ( 36) link_ALPHA1-3 : bond 0.00972 / 0.59 ( 15) link_ALPHA1-3 : angle 3.12111 / 2.05 ( 45) link_ALPHA1-6 : bond 0.00484 / 0.31 ( 21) link_ALPHA1-6 : angle 1.44665 / 0.95 ( 63) link_BETA1-4 : bond 0.00679 / 0.45 ( 60) link_BETA1-4 : angle 2.47702 / 1.88 ( 180) link_NAG-ASN : bond 0.00333 / 0.20 ( 51) link_NAG-ASN : angle 2.46196 / 1.61 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7110 (tpm170) REVERT: A 225 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7905 (mt) REVERT: A 392 ASN cc_start: 0.4690 (t0) cc_final: 0.4301 (t0) REVERT: H 30 ARG cc_start: 0.8378 (ttp80) cc_final: 0.7805 (tpp80) REVERT: H 77 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7699 (mm) REVERT: H 100 LYS cc_start: 0.8146 (mttt) cc_final: 0.7887 (mtpp) REVERT: L 25 GLU cc_start: 0.7742 (pp20) cc_final: 0.7429 (pp20) REVERT: C 69 TRP cc_start: 0.8665 (m-90) cc_final: 0.8427 (m-90) REVERT: C 428 GLN cc_start: 0.8751 (mp10) cc_final: 0.7977 (mp10) REVERT: N 13 LYS cc_start: 0.8219 (mmtt) cc_final: 0.8005 (mmmt) REVERT: N 77 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7540 (mm) REVERT: N 100 LYS cc_start: 0.8211 (mttt) cc_final: 0.7935 (mtpp) REVERT: M 25 GLU cc_start: 0.7549 (pp20) cc_final: 0.7278 (pp20) REVERT: E 99 ASN cc_start: 0.8136 (t0) cc_final: 0.7890 (t0) REVERT: E 217 TYR cc_start: 0.8464 (m-10) cc_final: 0.8187 (m-10) REVERT: F 530 MET cc_start: 0.5541 (mtt) cc_final: 0.5066 (mtt) REVERT: P 13 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7816 (mmmt) REVERT: P 66 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6999 (ptm-80) REVERT: P 77 LEU cc_start: 0.7824 (mm) cc_final: 0.7534 (mm) REVERT: P 81 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7070 (mtt90) REVERT: P 100 LYS cc_start: 0.8150 (mttt) cc_final: 0.7823 (mtpp) outliers start: 48 outliers final: 29 residues processed: 326 average time/residue: 0.1339 time to fit residues: 66.9895 Evaluate side-chains 305 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139274 restraints weight = 29925.691| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.78 r_work: 0.3326 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21432 Z= 0.159 Angle : 0.721 11.506 29421 Z= 0.336 Chirality : 0.047 0.333 3723 Planarity : 0.005 0.083 3429 Dihedral : 4.849 25.009 2538 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.18 % Allowed : 11.92 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2325 helix: 0.80 (0.28), residues: 369 sheet: 0.26 (0.20), residues: 585 loop : -0.15 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 30 TYR 0.012 0.001 TYR L 49 PHE 0.018 0.002 PHE H 100K TRP 0.032 0.002 TRP B 610 HIS 0.006 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (21234) covalent geometry : angle 0.64854 / 0.32 (28866) SS BOND : bond 0.00391 / 0.26 ( 39) SS BOND : angle 1.54989 / 1.03 ( 78) hydrogen bonds : bond 0.03553 / 2.33 ( 689) hydrogen bonds : angle 5.47014 / 3.79 ( 1842) link_ALPHA1-2 : bond 0.01035 / 0.66 ( 12) link_ALPHA1-2 : angle 2.88406 / 1.84 ( 36) link_ALPHA1-3 : bond 0.00918 / 0.55 ( 15) link_ALPHA1-3 : angle 3.05010 / 2.00 ( 45) link_ALPHA1-6 : bond 0.00390 / 0.26 ( 21) link_ALPHA1-6 : angle 1.48859 / 0.99 ( 63) link_BETA1-4 : bond 0.00658 / 0.43 ( 60) link_BETA1-4 : angle 2.48167 / 1.88 ( 180) link_NAG-ASN : bond 0.00361 / 0.24 ( 51) link_NAG-ASN : angle 2.56623 / 1.69 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7708 (mmm160) cc_final: 0.7119 (tpm170) REVERT: A 225 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 392 ASN cc_start: 0.4698 (t0) cc_final: 0.4340 (t0) REVERT: H 30 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7716 (tpp80) REVERT: H 77 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7885 (mm) REVERT: H 100 LYS cc_start: 0.8108 (mttt) cc_final: 0.7831 (mtpp) REVERT: L 25 GLU cc_start: 0.7605 (pp20) cc_final: 0.7300 (pp20) REVERT: C 66 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7613 (mtm110) REVERT: C 69 TRP cc_start: 0.8658 (m-90) cc_final: 0.8392 (m-90) REVERT: C 92 ASN cc_start: 0.7591 (m-40) cc_final: 0.7339 (t0) REVERT: C 428 GLN cc_start: 0.8783 (mp10) cc_final: 0.7955 (mp10) REVERT: D 530 MET cc_start: 0.5756 (mtt) cc_final: 0.5421 (mtt) REVERT: N 13 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8043 (mmmt) REVERT: N 77 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7534 (mm) REVERT: N 100 LYS cc_start: 0.8175 (mttt) cc_final: 0.7930 (mtpp) REVERT: E 99 ASN cc_start: 0.8136 (t0) cc_final: 0.7897 (t0) REVERT: E 486 TYR cc_start: 0.7695 (m-10) cc_final: 0.7343 (m-10) REVERT: F 530 MET cc_start: 0.5890 (mtt) cc_final: 0.5495 (mtt) REVERT: F 608 VAL cc_start: 0.8361 (m) cc_final: 0.8093 (p) REVERT: P 13 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7880 (mmmt) REVERT: P 77 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7522 (mm) REVERT: P 100 LYS cc_start: 0.8270 (mttt) cc_final: 0.7961 (mtpp) outliers start: 46 outliers final: 29 residues processed: 315 average time/residue: 0.1318 time to fit residues: 63.4081 Evaluate side-chains 296 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 106 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134685 restraints weight = 29961.875| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.87 r_work: 0.3334 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21432 Z= 0.140 Angle : 0.696 9.673 29421 Z= 0.324 Chirality : 0.047 0.319 3723 Planarity : 0.005 0.083 3429 Dihedral : 4.774 26.326 2538 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.23 % Allowed : 12.06 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2325 helix: 0.82 (0.28), residues: 369 sheet: 0.70 (0.21), residues: 528 loop : -0.23 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 30 TYR 0.010 0.001 TYR P 91 PHE 0.016 0.002 PHE E 159 TRP 0.024 0.001 TRP D 610 HIS 0.008 0.001 HIS N 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21234) covalent geometry : angle 0.62754 / 0.31 (28866) SS BOND : bond 0.00386 / 0.26 ( 39) SS BOND : angle 1.41192 / 0.94 ( 78) hydrogen bonds : bond 0.03376 / 2.23 ( 689) hydrogen bonds : angle 5.36179 / 3.71 ( 1842) link_ALPHA1-2 : bond 0.01020 / 0.63 ( 12) link_ALPHA1-2 : angle 2.78193 / 1.76 ( 36) link_ALPHA1-3 : bond 0.00928 / 0.55 ( 15) link_ALPHA1-3 : angle 2.98089 / 1.96 ( 45) link_ALPHA1-6 : bond 0.00416 / 0.27 ( 21) link_ALPHA1-6 : angle 1.45368 / 0.96 ( 63) link_BETA1-4 : bond 0.00647 / 0.43 ( 60) link_BETA1-4 : angle 2.41769 / 1.83 ( 180) link_NAG-ASN : bond 0.00326 / 0.20 ( 51) link_NAG-ASN : angle 2.35669 / 1.57 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8049 (mt) REVERT: A 392 ASN cc_start: 0.4357 (t0) cc_final: 0.4067 (t0) REVERT: B 535 MET cc_start: 0.8283 (mmp) cc_final: 0.8059 (tpp) REVERT: H 30 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8169 (tpp80) REVERT: H 77 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7926 (mm) REVERT: H 100 LYS cc_start: 0.8190 (mttt) cc_final: 0.7907 (mtpp) REVERT: L 25 GLU cc_start: 0.7591 (pp20) cc_final: 0.7262 (pp20) REVERT: C 66 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7658 (mtm110) REVERT: C 69 TRP cc_start: 0.8651 (m-90) cc_final: 0.8308 (m-90) REVERT: C 92 ASN cc_start: 0.7665 (m-40) cc_final: 0.7368 (t0) REVERT: D 530 MET cc_start: 0.5930 (mtt) cc_final: 0.5625 (mtt) REVERT: N 13 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7959 (mmmt) REVERT: N 77 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7537 (mm) REVERT: N 81 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7184 (mtm110) REVERT: N 100 LYS cc_start: 0.8233 (mttt) cc_final: 0.7989 (mtpp) REVERT: E 99 ASN cc_start: 0.8115 (t0) cc_final: 0.7867 (t0) REVERT: E 486 TYR cc_start: 0.7662 (m-10) cc_final: 0.7335 (m-10) REVERT: F 530 MET cc_start: 0.6050 (mtt) cc_final: 0.5717 (mtt) REVERT: F 608 VAL cc_start: 0.8353 (m) cc_final: 0.8125 (p) REVERT: P 13 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7868 (mmmt) REVERT: P 77 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7569 (mm) REVERT: P 100 LYS cc_start: 0.8320 (mttt) cc_final: 0.7995 (mtpp) outliers start: 47 outliers final: 28 residues processed: 314 average time/residue: 0.1484 time to fit residues: 71.6632 Evaluate side-chains 298 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 575 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135698 restraints weight = 29984.490| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.89 r_work: 0.3319 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21432 Z= 0.158 Angle : 0.713 12.410 29421 Z= 0.333 Chirality : 0.047 0.308 3723 Planarity : 0.005 0.084 3429 Dihedral : 4.752 23.606 2538 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 12.16 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2325 helix: 0.74 (0.28), residues: 369 sheet: 0.60 (0.21), residues: 543 loop : -0.28 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 30 TYR 0.011 0.001 TYR L 49 PHE 0.018 0.002 PHE H 100K TRP 0.018 0.002 TRP D 610 HIS 0.007 0.001 HIS N 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (21234) covalent geometry : angle 0.64252 / 0.32 (28866) SS BOND : bond 0.00421 / 0.28 ( 39) SS BOND : angle 1.49182 / 0.98 ( 78) hydrogen bonds : bond 0.03430 / 2.26 ( 689) hydrogen bonds : angle 5.38585 / 3.72 ( 1842) link_ALPHA1-2 : bond 0.01024 / 0.63 ( 12) link_ALPHA1-2 : angle 2.76842 / 1.75 ( 36) link_ALPHA1-3 : bond 0.00936 / 0.55 ( 15) link_ALPHA1-3 : angle 2.92621 / 1.93 ( 45) link_ALPHA1-6 : bond 0.00388 / 0.25 ( 21) link_ALPHA1-6 : angle 1.46084 / 0.97 ( 63) link_BETA1-4 : bond 0.00636 / 0.42 ( 60) link_BETA1-4 : angle 2.40560 / 1.81 ( 180) link_NAG-ASN : bond 0.00341 / 0.23 ( 51) link_NAG-ASN : angle 2.56970 / 1.66 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7927 (mt) REVERT: A 392 ASN cc_start: 0.4593 (t0) cc_final: 0.4306 (t0) REVERT: H 30 ARG cc_start: 0.8438 (ttp80) cc_final: 0.7810 (tpp80) REVERT: H 77 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7936 (mm) REVERT: H 100 LYS cc_start: 0.8211 (mttt) cc_final: 0.7937 (mtpp) REVERT: C 66 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.7814 (mtm110) REVERT: C 69 TRP cc_start: 0.8655 (m-90) cc_final: 0.8319 (m-90) REVERT: C 426 MET cc_start: 0.8286 (mtp) cc_final: 0.8040 (mtp) REVERT: D 530 MET cc_start: 0.5940 (mtt) cc_final: 0.5685 (mtt) REVERT: N 13 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7839 (mmmt) REVERT: N 77 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7623 (mm) REVERT: N 81 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7210 (mtm110) REVERT: N 100 LYS cc_start: 0.8182 (mttt) cc_final: 0.7897 (mtpp) REVERT: E 66 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8060 (mtm-85) REVERT: F 530 MET cc_start: 0.5880 (mtt) cc_final: 0.5476 (mtt) REVERT: F 608 VAL cc_start: 0.8403 (m) cc_final: 0.8190 (p) REVERT: F 626 MET cc_start: 0.6696 (mtp) cc_final: 0.6379 (ttm) REVERT: F 657 GLU cc_start: 0.8402 (mp0) cc_final: 0.7761 (mp0) REVERT: P 13 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7914 (mmmt) REVERT: P 77 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7522 (mm) REVERT: P 100 LYS cc_start: 0.8221 (mttt) cc_final: 0.7906 (mtpp) outliers start: 51 outliers final: 38 residues processed: 301 average time/residue: 0.1432 time to fit residues: 66.2561 Evaluate side-chains 304 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN L 50 ASN M 50 ASN E 300 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132791 restraints weight = 29785.506| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.74 r_work: 0.3267 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21432 Z= 0.254 Angle : 0.816 11.879 29421 Z= 0.384 Chirality : 0.051 0.341 3723 Planarity : 0.005 0.085 3429 Dihedral : 5.131 24.412 2538 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.28 % Allowed : 12.49 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2325 helix: 0.44 (0.28), residues: 369 sheet: 0.43 (0.21), residues: 531 loop : -0.51 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 30 TYR 0.018 0.002 TYR M 87 PHE 0.026 0.003 PHE H 100K TRP 0.023 0.002 TRP D 571 HIS 0.016 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.25 (21234) covalent geometry : angle 0.74866 / 0.37 (28866) SS BOND : bond 0.00703 / 0.42 ( 39) SS BOND : angle 1.82508 / 1.22 ( 78) hydrogen bonds : bond 0.04105 / 2.69 ( 689) hydrogen bonds : angle 5.79373 / 3.98 ( 1842) link_ALPHA1-2 : bond 0.00839 / 0.52 ( 12) link_ALPHA1-2 : angle 2.93896 / 1.87 ( 36) link_ALPHA1-3 : bond 0.00840 / 0.48 ( 15) link_ALPHA1-3 : angle 2.87488 / 1.90 ( 45) link_ALPHA1-6 : bond 0.00356 / 0.22 ( 21) link_ALPHA1-6 : angle 1.51082 / 1.01 ( 63) link_BETA1-4 : bond 0.00588 / 0.39 ( 60) link_BETA1-4 : angle 2.56514 / 1.91 ( 180) link_NAG-ASN : bond 0.00565 / 0.39 ( 51) link_NAG-ASN : angle 2.74084 / 1.82 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8069 (mt) REVERT: H 30 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8226 (tpp80) REVERT: H 77 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8037 (mm) REVERT: H 100 LYS cc_start: 0.8272 (mttt) cc_final: 0.7972 (mtpp) REVERT: C 66 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7751 (mtm110) REVERT: N 77 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7720 (mm) REVERT: N 81 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7227 (mtm110) REVERT: N 100 LYS cc_start: 0.8245 (mttt) cc_final: 0.7944 (mtpp) REVERT: E 159 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: E 350 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6366 (tpp-160) REVERT: E 411 ASN cc_start: 0.7094 (p0) cc_final: 0.6766 (p0) REVERT: F 657 GLU cc_start: 0.8511 (mp0) cc_final: 0.7873 (mp0) REVERT: P 13 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7948 (mmmt) REVERT: P 77 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7632 (mm) REVERT: P 100 LYS cc_start: 0.8364 (mttt) cc_final: 0.8003 (mtpp) outliers start: 48 outliers final: 36 residues processed: 296 average time/residue: 0.1466 time to fit residues: 66.6836 Evaluate side-chains 288 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 141 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 147 optimal weight: 0.0970 chunk 177 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN F 650 GLN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133479 restraints weight = 30185.223| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.14 r_work: 0.3284 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21432 Z= 0.155 Angle : 0.729 9.764 29421 Z= 0.343 Chirality : 0.047 0.314 3723 Planarity : 0.004 0.089 3429 Dihedral : 4.951 24.562 2538 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 13.06 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2325 helix: 0.51 (0.28), residues: 369 sheet: 0.36 (0.21), residues: 555 loop : -0.44 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 20 TYR 0.011 0.001 TYR H 100O PHE 0.016 0.002 PHE N 100K TRP 0.016 0.002 TRP D 610 HIS 0.008 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (21234) covalent geometry : angle 0.66265 / 0.33 (28866) SS BOND : bond 0.00403 / 0.26 ( 39) SS BOND : angle 1.63799 / 1.13 ( 78) hydrogen bonds : bond 0.03526 / 2.32 ( 689) hydrogen bonds : angle 5.51332 / 3.81 ( 1842) link_ALPHA1-2 : bond 0.00833 / 0.50 ( 12) link_ALPHA1-2 : angle 2.69225 / 1.69 ( 36) link_ALPHA1-3 : bond 0.00897 / 0.53 ( 15) link_ALPHA1-3 : angle 2.85316 / 1.88 ( 45) link_ALPHA1-6 : bond 0.00406 / 0.26 ( 21) link_ALPHA1-6 : angle 1.45129 / 0.96 ( 63) link_BETA1-4 : bond 0.00590 / 0.38 ( 60) link_BETA1-4 : angle 2.38766 / 1.78 ( 180) link_NAG-ASN : bond 0.00344 / 0.23 ( 51) link_NAG-ASN : angle 2.51930 / 1.68 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7978 (ttp80) REVERT: A 225 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 392 ASN cc_start: 0.4838 (t0) cc_final: 0.4509 (t0) REVERT: B 614 TRP cc_start: 0.6075 (m-10) cc_final: 0.5846 (m-10) REVERT: H 30 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8052 (tpp80) REVERT: H 77 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8027 (mm) REVERT: H 100 LYS cc_start: 0.8244 (mttt) cc_final: 0.7961 (mtpp) REVERT: L 20 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.7061 (mmm-85) REVERT: L 25 GLU cc_start: 0.7452 (pp20) cc_final: 0.7202 (pp20) REVERT: C 66 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7772 (mtm110) REVERT: C 69 TRP cc_start: 0.8668 (m-90) cc_final: 0.8320 (m-90) REVERT: N 77 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7768 (mm) REVERT: N 81 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7294 (mtm110) REVERT: N 100 LYS cc_start: 0.8323 (mttt) cc_final: 0.8022 (mtpp) REVERT: M 25 GLU cc_start: 0.7349 (pp20) cc_final: 0.6886 (pp20) REVERT: E 411 ASN cc_start: 0.7100 (p0) cc_final: 0.6769 (p0) REVERT: F 540 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5482 (mt0) REVERT: F 657 GLU cc_start: 0.8518 (mp0) cc_final: 0.7853 (mp0) REVERT: P 13 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7950 (mmmt) REVERT: P 77 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7658 (mm) REVERT: P 100 LYS cc_start: 0.8332 (mttt) cc_final: 0.7983 (mtpp) outliers start: 40 outliers final: 32 residues processed: 291 average time/residue: 0.1354 time to fit residues: 60.4957 Evaluate side-chains 291 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131357 restraints weight = 30168.030| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.21 r_work: 0.3256 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21432 Z= 0.203 Angle : 0.771 16.065 29421 Z= 0.361 Chirality : 0.049 0.383 3723 Planarity : 0.005 0.088 3429 Dihedral : 5.018 22.609 2538 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.09 % Allowed : 13.15 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2325 helix: 0.40 (0.28), residues: 369 sheet: 0.31 (0.21), residues: 555 loop : -0.51 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 20 TYR 0.013 0.002 TYR M 49 PHE 0.021 0.002 PHE N 100K TRP 0.017 0.002 TRP D 571 HIS 0.012 0.001 HIS P 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (21234) covalent geometry : angle 0.70015 / 0.35 (28866) SS BOND : bond 0.00485 / 0.31 ( 39) SS BOND : angle 1.73317 / 1.14 ( 78) hydrogen bonds : bond 0.03733 / 2.46 ( 689) hydrogen bonds : angle 5.60840 / 3.87 ( 1842) link_ALPHA1-2 : bond 0.00813 / 0.49 ( 12) link_ALPHA1-2 : angle 2.71895 / 1.71 ( 36) link_ALPHA1-3 : bond 0.00868 / 0.50 ( 15) link_ALPHA1-3 : angle 2.83282 / 1.87 ( 45) link_ALPHA1-6 : bond 0.00363 / 0.24 ( 21) link_ALPHA1-6 : angle 1.47764 / 0.99 ( 63) link_BETA1-4 : bond 0.00574 / 0.38 ( 60) link_BETA1-4 : angle 2.42095 / 1.80 ( 180) link_NAG-ASN : bond 0.00435 / 0.30 ( 51) link_NAG-ASN : angle 2.90869 / 1.92 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4186.54 seconds wall clock time: 73 minutes 3.01 seconds (4383.01 seconds total)